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Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes Roxana Yockteng, Sylvain Marthey, Hélène Chiapello, Annie Gendrault, Michael Hood, Francois Rodolphe, Benjamin Devier, Patrick Wincker, Carole Dossat, Tatiana Giraud To cite this version: Roxana Yockteng, Sylvain Marthey, Hélène Chiapello, Annie Gendrault, Michael Hood, et al.. Ex- pressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes. BMC Genomics, BioMed Central, 2009, 8 (1), pp.272. 10.1186/1471-2164-8- 272. hal-02333218 HAL Id: hal-02333218 https://hal.archives-ouvertes.fr/hal-02333218 Submitted on 31 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. BMC Genomics BioMed Central Research article Open Access Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes Roxana Yockteng1,2, Sylvain Marthey3, Hélène Chiapello3, Annie Gendrault3, Michael E Hood4, François Rodolphe3, Benjamin Devier1, Patrick Wincker5, Carole Dossat5 and Tatiana Giraud*1 Address: 1UMR 8079 CNRS-UPS, Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405 Orsay Cedex, France, 2UMR 5202, CNRS-MNHN, Origine, Structure et Evolution de la Biodiversité, Département Systématique et Evolution, 16 rue Buffon CP 39, 75005, Paris, France, 3INRA, Unité Mathématique, Informatique et Génome, Domaine Vilvert, Jouy-en-Josas, F-78352, France, 4Department of Biology, Amherst College, Amherst, MA 01002, USA and 5Génoscope, UMR CNRS 8030, 2 Gaston Crémieux, CP 5706, 91507 Evry, France Email: Roxana Yockteng - [email protected]; Sylvain Marthey - [email protected]; Hélène Chiapello - [email protected]; Annie Gendrault - [email protected]; Michael E Hood - [email protected]; François Rodolphe - [email protected]; Benjamin Devier - [email protected]; Patrick Wincker - [email protected]; Carole Dossat - [email protected]; Tatiana Giraud* - [email protected] * Corresponding author Published: 10 August 2007 Received: 17 November 2006 Accepted: 10 August 2007 BMC Genomics 2007, 8:272 doi:10.1186/1471-2164-8-272 This article is available from: http://www.biomedcentral.com/1471-2164/8/272 © 2007 Yockteng et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The basidiomycete fungus Microbotryum violaceum is responsible for the anther-smut disease in many plants of the Caryophyllaceae family and is a model in genetics and evolutionary biology. Infection is initiated by dikaryotic hyphae produced after the conjugation of two haploid sporidia of opposite mating type. This study describes M. violaceum ESTs corresponding to nuclear genes expressed during conjugation and early hyphal production. Results: A normalized cDNA library generated 24,128 sequences, which were assembled into 7,765 unique genes; 25.2% of them displayed significant similarity to annotated proteins from other organisms, 74.3% a weak similarity to the same set of known proteins, and 0.5% were orphans. We identified putative pheromone receptors and genes that in other fungi are involved in the mating process. We also identified many sequences similar to genes known to be involved in pathogenicity in other fungi. The M. violaceum EST database, MICROBASE, is available on the Web and provides access to the sequences, assembled contigs, annotations and programs to compare similarities against MICROBASE. Conclusion: This study provides a basis for cloning the mating type locus, for further investigation of pathogenicity genes in the anther smut fungi, and for comparative genomics. Background the evolution of host-pathogen interactions, thereby Deciphering the molecular mechanisms involved in infec- advancing our understanding of host specificity, viru- tion is important for the control of devastating crop dis- lence, and the emergence of new diseases. Modern eases. Furthermore, the comparison of pathogenicity- sequencing technologies have led to a remarkable increase related genes from different fungi provides insight into in genomic data available for identifying genes by similar- Page 1 of 12 (page number not for citation purposes) BMC Genomics 2007, 8:272 http://www.biomedcentral.com/1471-2164/8/272 ity searches [1]. Key genes involved in pathogenicity in human activities, making it valuable for the study of nat- several fungi have been compiled into the PHI database ural host-pathogen coevolution, and avoiding the risk of [2]. dispersion in human crops. However, one present limita- tion of this model is that little genomic sequence data are In the smut fungi of monocot hosts (e.g. Ustilago maydis available, except studies on transposable elements and on and U. hordei, major pathogens of corn and barley, respec- the genomic defense mechanism against the accumula- tively), the sexual phase and the genes linked to the mat- tion of mobile elements [12]. In particular, the mating- ing-type loci play a key role in development and type locus was reticent to several cloning attempts (T. pathogenicity [3]. Mating-type loci determine sexual com- Giraud and M.E. Hood, unpublished; J. Kronstad, pers. patibility: only individuals differing at these loci can mate. com.) and there exist few sequences of expressed genes In U. maydis, cell recognition and fusion is regulated by a from M. violaceum in public databases. Only a few Micro- pheromone/receptor system that resides at the a locus. botryum genes that contribute to hyphal development and After fusion, the dikaryon is maintained and cells switch subsequent infectious capability have been described to filamentous growth if they are heterozygous for the sec- [13]. ond mating type locus, the b locus [4,5]. The b locus encodes two homeodomain proteins that function as The generation of Expressed Sequence Tags (EST) is an transcriptional regulators after dimerization. The majority efficient tool to discover novel genes and investigate their of sexual basidiomycete fungi possess such a system called expression at different developmental stages (e.g., "tetrapolar", where a and b unlinked loci (respectively [14,15]). Therefore, a cDNA library has been built from called B and A in some species) are both involved in sex- pools of mating haploid cells and growing infectious ual compatibility and are often multiallelic [5,6]. Other hyphae for a single dikaryotic isolate of M. violaceum col- members of this phylum are "bipolar", due to the a and b lected from the host plant species Silene latifolia. Genes loci being tightly linked (e.g. in U. hordei, [7]) or due to involved in mating and during early pathogenic develop- one of the two mating type loci having lost their role in ment were expected to be expressed under these condi- mating type specificity (e.g. in Coprinellus disseminatus, tions because they represent the mating and infectious [8]). Tetrapolarity is likely ancestral [9] and promotes out- stages. We generated 24,128 ESTs from this library, on crossing as it increases the number of available mating which we performed similarity searches in order to iden- type. The study of mating-type loci is important for under- tify genes with functions known as important for these standing the infection process and the evolution of mat- developmental stages. ing systems in basidiomycetes. Results and discussion A widely recognized model to study host-pathogen coev- EST sequence analysis olution and fungal genetics is the anther smut fungus The cDNA library created from poly(A)+mRNA from Microbotryum violaceum (Pers.) Deml and Oberw. (for- seven days-old mixed A1 and A2 cultures produced merly Ustilago violacea (Pers.) Fuckel), which is a basidio- enough material to sequence 40,000 clones. A total of mycete, obligate parasite of more than 100 perennial 28,430 sequences were obtained (success rate of 71%) species of Caryophyllaceae [10]. In plants infected by M. with an average read length of 815 bp, which is similar to violaceum, fungal teliospores are produced in anthers and the EST library of U. maydis [14]. Some ribosomal (n = diseased plants are usually completely sterilized, the pol- 109), mitochondrial (n = 16) and vector (n = 14) len being replaced by fungal spores and the stigmas and sequences were identified. After discarding them, a total ovaries being reduced. New infections occur when fungal of 24,128 ESTs were obtained (85% of the initial spores are transported from a diseased to a healthy plant sequences). After trimming vector and low quality by the insects that usually serve as pollinators. Once sequences, the average cDNA read was not very long, with deposited on a host plant, diploid teliospores undergo 345 ± 167 bases (mean ± SD). We indeed did not select meiosis and give rise to four haploid cells, two of mating the sizes of mRNA, as recommended for normalized type A1 and two of mating-type A2, M. violaceum having a libraries. bipolar mating system. Each of these post-meiotic cells can buds off yeast-like sporidia on the plant surface. New These 24,128 ESTs were assembled into 4,178 contigs infectious dikaryons are produced only after conjugation while 3,587 remained as singlets (Figure 1). This corre- of two cells of opposite mating-types [11]. The fungus sponds to a redundancy of 85% (number of ESTs assem- then grows endophytically and causes perennial systemic bled in clusters/total number of ESTs), which is very high infections.
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    Oikos 123: 1126–1136, 2014 doi: 10.1111/oik.01001 © 2014 Th e Authors. Oikos © 2014 Nordic Society Oikos Subject Editor: Anna-Liisa Laine. Accepted 14 February 2014 Elevational disease distribution in a natural plant – pathogen system: insights from changes across host populations and climate Jessica L. Abbate and Janis Antonovics J. L. Abbate ([email protected]), Centre d ’ É cologie Fonctionelle et É volutive (CEFE), UMR 5175, CNRS, 1919 route de Mende, FR-34293, Montpellier, France. – J. Antonovics, Dept of Biology, Univ. of Virginia, Charlottesville, VA 22904, USA. Understanding the factors determining the distribution of parasites and pathogens in natural systems is essential for making predictions about the spread of emerging infectious disease. Here, we report the distribution of the fungal anther-smut disease, caused by Microbotryum spp., on populations of the European wildfl ower Silene vulgaris over a range of elevations. A survey of several geographically distinct mountains in the southern French alps found that anther- smut disease was restricted to high elevations, rarely observed below 1300 m despite availability of hosts below this elevation. Anther smut causes host-sterility, and is recognized as a model system for natural host – pathogen interactions, sharing common features with vector-borne and sexually-transmitted disease in animals. In such systems, many biotic and abiotic factors likely to change over ecological gradients can infl uence disease epidemiology, including host spatial structure, pathogen infectivity, host resistance, and vector behavior. Here, we tested whether host population size, density, or connectivity also declined across elevation, and whether these epidemiologically relevant factors explained the observed disease distribution.
  • Identification and Functional Characterization of Effectors from an Anther Smut Fungus, Microbotryum Lychnidis-Dioicae

    Identification and Functional Characterization of Effectors from an Anther Smut Fungus, Microbotryum Lychnidis-Dioicae

    University of Louisville ThinkIR: The University of Louisville's Institutional Repository Electronic Theses and Dissertations 12-2018 Identification and functional characterization of effectors from an anther smut fungus, Microbotryum lychnidis-dioicae. Venkata Swathi Kuppireddy University of Louisville Follow this and additional works at: https://ir.library.louisville.edu/etd Part of the Molecular Genetics Commons Recommended Citation Kuppireddy, Venkata Swathi, "Identification and functional characterization of effectors from an anther smut fungus, Microbotryum lychnidis-dioicae." (2018). Electronic Theses and Dissertations. Paper 3078. https://doi.org/10.18297/etd/3078 This Doctoral Dissertation is brought to you for free and open access by ThinkIR: The University of Louisville's Institutional Repository. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of ThinkIR: The University of Louisville's Institutional Repository. This title appears here courtesy of the author, who has retained all other copyrights. For more information, please contact [email protected]. IDENTIFICATION AND FUNCTIONAL CHARACTERIZATION OF EFFECTORS FROM AN ANTHER SMUT FUNGUS, MICROBOTRYUM LYCHNIDIS-DIOICAE By Venkata Swathi Kuppireddy M.Sc., Biology, University of Louisville, 2016 A Dissertation Submitted to the Faculty of the College of Arts and Sciences of the University of Louisville in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biology Department of Biology, Division of Molecular, Cellular and Developmental Biology, University of Louisville Louisville, Kentucky December 2018 Copyright 2018 by Venkata Swathi Kuppireddy © All rights reserved IDENTIFICATION AND FUNCTIONAL CHARACTERIZATION OF EFFECTORS FROM AN ANTHER SMUT FUNGUS, MICROBOTRYUM LYCHNIDIS-DIOICAE By Venkata Swathi Kuppireddy M.Sc., Biology, University of Louisville, 2016 A Dissertation Approved on November 14, 2018 By the following Dissertation Committee: _________________________________________ Dr.